
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:22 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip" (19 taxa, 588 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: HKYG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
HKYIG	41	-2138.4907	4365.2890	0.7673	0.7673
HKYG	40	-2140.9723	4367.9410	0.2037	0.9710
GTRIG	45	-2137.7030	4373.0444	0.0159	0.9869
HKYI	40	-2144.4152	4374.8267	0.0065	0.9934
GTRG	44	-2139.7786	4374.8500	0.0064	0.9998
GTRI	44	-2143.3711	4382.0350	0.0002	1.0000
K2PIG	38	-2156.1320	4393.6630	0.0000	1.0000
K2PG	37	-2157.9943	4395.1013	0.0000	1.0000
SYMIG	42	-2153.0345	4396.6966	0.0000	1.0000
SYMG	41	-2154.6679	4397.6434	0.0000	1.0000
K2PI	37	-2161.5138	4402.1404	0.0000	1.0000
SYMI	41	-2158.7730	4405.8537	0.0000	1.0000
F81IG	40	-2176.0294	4438.0552	0.0000	1.0000
F81G	39	-2177.8411	4439.3756	0.0000	1.0000
F81I	39	-2181.5852	4446.8638	0.0000	1.0000
JC69IG	37	-2191.0966	4461.3059	0.0000	1.0000
JC69G	36	-2192.7939	4462.4227	0.0000	1.0000
JC69I	36	-2196.6282	4470.0912	0.0000	1.0000
HKY	39	-2241.9682	4567.6298	0.0000	1.0000
GTR	43	-2241.0504	4575.0566	0.0000	1.0000
K2P	36	-2257.6229	4592.0805	0.0000	1.0000
SYM	40	-2255.0616	4596.1196	0.0000	1.0000
F81	38	-2273.9418	4629.2825	0.0000	1.0000
JC69	35	-2288.1143	4650.7939	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2138.4907	4358.9813	0.7759	0.7759
HKYG	40	-2140.9723	4361.9446	0.1763	0.9522
GTRIG	45	-2137.7030	4365.4060	0.0312	0.9834
GTRG	44	-2139.7786	4367.5572	0.0107	0.9941
HKYI	40	-2144.4152	4368.8303	0.0056	0.9997
GTRI	44	-2143.3711	4374.7422	0.0003	1.0000
K2PIG	38	-2156.1320	4388.2641	0.0000	1.0000
K2PG	37	-2157.9943	4389.9886	0.0000	1.0000
SYMIG	42	-2153.0345	4390.0690	0.0000	1.0000
SYMG	41	-2154.6679	4391.3357	0.0000	1.0000
K2PI	37	-2161.5138	4397.0277	0.0000	1.0000
SYMI	41	-2158.7730	4399.5460	0.0000	1.0000
F81IG	40	-2176.0294	4432.0589	0.0000	1.0000
F81G	39	-2177.8411	4433.6821	0.0000	1.0000
F81I	39	-2181.5852	4441.1704	0.0000	1.0000
JC69IG	37	-2191.0966	4456.1932	0.0000	1.0000
JC69G	36	-2192.7939	4457.5879	0.0000	1.0000
JC69I	36	-2196.6282	4465.2564	0.0000	1.0000
HKY	39	-2241.9682	4561.9364	0.0000	1.0000
GTR	43	-2241.0504	4568.1007	0.0000	1.0000
K2P	36	-2257.6229	4587.2457	0.0000	1.0000
SYM	40	-2255.0616	4590.1232	0.0000	1.0000
F81	38	-2273.9418	4623.8836	0.0000	1.0000
JC69	35	-2288.1143	4646.2286	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2140.9723	4537.0137	0.6553	0.6553
HKYIG	41	-2138.4907	4538.4271	0.3232	0.9785
HKYI	40	-2144.4152	4543.8994	0.0210	0.9995
K2PG	37	-2157.9943	4551.9275	0.0004	0.9999
K2PIG	38	-2156.1320	4554.5797	0.0001	1.0000
K2PI	37	-2161.5138	4558.9666	0.0000	1.0000
GTRG	44	-2139.7786	4560.1332	0.0000	1.0000
GTRIG	45	-2137.7030	4562.3588	0.0000	1.0000
GTRI	44	-2143.3711	4567.3182	0.0000	1.0000
SYMG	41	-2154.6679	4570.7815	0.0000	1.0000
SYMIG	42	-2153.0345	4573.8916	0.0000	1.0000
SYMI	41	-2158.7730	4578.9918	0.0000	1.0000
F81G	39	-2177.8411	4604.3745	0.0000	1.0000
F81IG	40	-2176.0294	4607.1280	0.0000	1.0000
F81I	39	-2181.5852	4611.8627	0.0000	1.0000
JC69G	36	-2192.7939	4615.1500	0.0000	1.0000
JC69IG	37	-2191.0966	4618.1321	0.0000	1.0000
JC69I	36	-2196.6282	4622.8186	0.0000	1.0000
HKY	39	-2241.9682	4732.6288	0.0000	1.0000
K2P	36	-2257.6229	4744.8079	0.0000	1.0000
GTR	43	-2241.0504	4756.3000	0.0000	1.0000
SYM	40	-2255.0616	4765.1923	0.0000	1.0000
F81	38	-2273.9418	4790.1992	0.0000	1.0000
JC69	35	-2288.1143	4799.4141	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip = 1 - 588;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip = 1 - 588;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip = 1 - 588;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_17221.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

